chomp @INFILE2 loop. You are right, I should have chomped the lines. Because I get that file by using another script where I add \n at the end. Thanks for pointing it out.

I revised the code in line with your suggestions, and get the following errors:

Possible unintended interpolation of @VariantList in string at PD.pl line 91.

I have no idea why I am getting this error. I thought I can safely use an array to print it out in this way.

Type of arg 1 to push must be array (not hash slice) at PD.pl line 33, near "$line;"

This is weird?!

Global symbol "@VariantList" requires explicit package name at PD.pl l
+ine 91.
Execution of PD.pl aborted due to compilation errors.
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And here is the code.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %info = (); 
my $humangi;

my $data = '/DATA/proteinfile.txt'; 
open INFILE, '<', $data or die "Failed at opening $data!\n";

# Construct the hash with GIs as keys and sequences as values
while ( <INFILE> ) {
my $line = $_;
chomp($line);
    last if m!END!;
    
    if($line=~m/HUMAN/){
        
        ($humangi) = ($line=~m/^\S+\|(\d+)/)
    
        }
    
    if($line=~m/^\S+\|(\d+)/)
       {
        if(defined($1))
         { 
          my $gi=$1;
         }    
       }
    else
       {
        if (defined(my $gi))
          {
          push (@info{$gi}, $line);
          }
        else
          {
          die "Badly formatted file. Failed at reading the GI!\n";
          }
       }
}
    #print Dumper (\%info);

    print "$humangi\n";

close(INFILE);

my $data2 = '/DATA/variantlist.txt'; 
open INFILE2, '<', $data2 or die "Failed at opening $data2!\n";

my $data3 = '/DATA/VariantOutput.txt'; 
open OUTFILE, '>', $data3 or die "Failed at opening $data3!\n";

while ( <INFILE2>){
# Grab a variant from the file (in this example: P82L)
my $line2 = $_;
chomp($line2);
my $Variant = $line2;

# Split the variant into three parts
my ($source, $position, $sink) = split(/(\d+)(\w)/, $Variant);

print "$source , $ position , $sink\n";
# Check whether HS has the source (i.e., P) at the given position (i.e
+., 82)
my @temp = @info{$humangi};

    if ( $temp[$position] eq $source) {
    
     print "Yep, $source has been confirmed!\n";
    }
    
    else {
        
    print "There is something wrong!\n";
    }

# Scan the rest of the sequences to check what amino acid they have at
+ the given position
for my $gi ( keys %info ) {
        my @value = @info{$gi};
        
        my @VariantList = ();
        
        push ( @VariantList, $value[$position]); 
        
        if ($value[$position] eq $sink){ # Note the cases where we obs
+erve the sink (i.e., L) at this position
            
            print OUTFILE "A pathogenic deviation has been found at si
+te $position - from $source to $sink !\n" . " And the corresponding g
+i for this deviation is: $gi\n";
            
            }
}

print OUTFILE "Variant list contains: @VariantList\n";
}
close(INFILE2);
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Oops, my bad. I should have used the hash slice correctly.

Changing  push (@info{$gi}, $line) to  push (@{$info{$gi}} solved the problem.

So I am left with the error involving @VariantList. Probably I am making another fundamental mistake when assigning, e.g., trying to assign an array into a scalar. I am looking into it.

Victory! I made the code work properly. Nevertheless, I do probably have efficiency problems. I would appreciate if you can comment on points where I can improve my code (in terms of both performance and appropriate style). Thanks guys, I could not do it without your help!

Here is the final ugly code.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %info = (); 
my ($gi, $humangi, $accession);

my $data = '/DATA/proteinfile.txt'; 
open INFILE, '<', $data or die "Failed at opening $data!\n";

# Construct the hash with GIs as keys and sequences as values
while ( <INFILE> ) {
my $line = $_;
chomp($line);
    last if m!END!;
    
    if($line=~m/HUMAN/){
        
        ($humangi) = ($line=~m/^\S+\|(\d+)/);
        
       ($accession) = ($line=~m/^\S+\|\d+\|\w+\|(\S{6}?)/);
       
          }
    
    if($line=~m/^\S+\|(\d+)/)
       {
        if(defined($1))
         { 
          $gi=$1;
         }    
       }
    else
       {
        $info{$gi} = $line;
        }
}
    #print Dumper (\%info);

    print "$humangi\n";
    print "$accession\n";

close(INFILE);

my $data2 = '/DATA/variantlist.txt'; 
open INFILE2, '<', $data2 or die "Failed at opening $data2!\n";

my $data3 = '/DATA/VariantOutput.txt'; 
open OUTFILE, '>', $data3 or die "Failed at opening $data3!\n";

print OUTFILE "This is [GI: $humangi] and [Accession: $accession]\nVAR
+IANT\t\tPOTENTIAL\t\tPD\n";

while ( <INFILE2>){
# Grab a variant from the file (in this example: P82L)
my $line2 = $_;
chomp($line2);
my $Variant = $line2;

# Split the variant into three parts
my ($source, $position, $sink) = split(/(\d+)(\w)/, $Variant);

#print "$source\t$position\t$sink\n";
# Check whether HS has the source (i.e., P) at the given position (i.e
+., 82)
my $temp = $info{$humangi};

    #print "Temp contains $temp" . "\n";
    
my @char = split //, $temp;    

    #print "Now \@char contains: @char";

    #print "Inside the temp: $char[0] and $char[1]\n";

my $target = $char[$position-1];
    
    #print "This is the target: $target" . "\n";

if ( $target eq $source) {
    
     print "Yep!\n";
    }
    
my @VariantList = ();
my @PDList = ();
    
# Scan the rest of the sequences to check what amino acid they have at
+ the given position
for my $gi ( keys %info ) {
        my $value = $info{$gi};
        
        my @char2 = split //, $value;
        
        my $potential = $char2[$position-1];
        
        push (@VariantList, $potential); 
        
        
        if ($potential eq $sink){ # Note the cases where we observe th
+e sink (i.e., L) at this position
            
            my $pd = "$potential" . "{" . "$gi" . "}";
            
            push (@PDList, $pd)             
            #print "A pathogenic deviation has been found at site $pos
+ition - from $source to $sink !\n" . " And the corresponding gi for t
+his deviation is: $gi\n";
            
            }
            }

print OUTFILE "$Variant\t\t@VariantList\t\t@PDList\n";
}
close(INFILE2);
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